chore(trainer): sample train set to base model importances on

src/gentropy/method/l2g/trainer.py

@@ -95,9 +95,9 @@ def fit(
             and self.y_train is not None
             and self.features_list is not None
         ):
-            assert self.x_train.size != 0 and self.y_train.size != 0, (
-                "Train data not set, nothing to fit."
-            )
+            assert (
+                self.x_train.size != 0 and self.y_train.size != 0
+            ), "Train data not set, nothing to fit."
             fitted_model = self.model.model.fit(X=self.x_train, y=self.y_train)
             self.model = LocusToGeneModel(
                 model=fitted_model,
@@ -112,7 +112,7 @@ def _get_shap_explanation(
         self: LocusToGeneTrainer,
         model: LocusToGeneModel,
     ) -> Explanation:
-        """Get the SHAP values for the given model and data. We pass the full X matrix (without the labels) to interpret their shap values.
+        """Get the SHAP values for the given model and data. We sample the full X matrix (without the labels) to interpret their shap values.
 
         Args:
             model (LocusToGeneModel): Model to explain.
@@ -133,12 +133,15 @@ def _get_shap_explanation(
                 model.model,
                 data=training_data,
                 feature_perturbation="interventional",
+                model_output="probability",
             )
             try:
-                return explainer(training_data)
+                return explainer(training_data.sample(n=1_000))
             except Exception as e:
                 if "Additivity check failed in TreeExplainer" in repr(e):
-                    return explainer(training_data, check_additivity=False)
+                    return explainer(
+                        training_data.sample(n=1_000), check_additivity=False
+                    )
                 else:
                     raise
 
@@ -191,9 +194,9 @@ def log_to_wandb(
             or self.features_list is None
         ):
             raise RuntimeError("Train data not set, we cannot log to W&B.")
-        assert self.x_train.size != 0 and self.y_train.size != 0, (
-            "Train data not set, nothing to evaluate."
-        )
+        assert (
+            self.x_train.size != 0 and self.y_train.size != 0
+        ), "Train data not set, nothing to evaluate."
         fitted_classifier = self.model.model
         y_predicted = fitted_classifier.predict(self.x_test)
         y_probas = fitted_classifier.predict_proba(self.x_test)